Literature DB >> 21164994

Incorrect support and missing center tolerances of phasing algorithms.

Xiaojing Huang1, Johanna Nelson, Jan Steinbrener, Janos Kirz, Joshua J Turner, Chris Jacobsen.   

Abstract

In x-ray diffraction microscopy, iterative algorithms retrieve reciprocal space phase information, and a real space image, from an object's coherent diffraction intensities through the use of a priori information such as a finite support constraint. In many experiments, the object's shape or support is not well known, and the diffraction pattern is incompletely measured. We describe here computer simulations to look at the effects of both of these possible errors when using several common reconstruction algorithms. Overly tight object supports prevent successful convergence; however, we show that this can often be recognized through pathological behavior of the phase retrieval transfer function. Dynamic range limitations often make it difficult to record the central speckles of the diffraction pattern. We show that this leads to increasing artifacts in the image when the number of missing central speckles exceeds about 10, and that the removal of unconstrained modes from the reconstructed image is helpful only when the number of missing central speckles is less than about 50. This simulation study helps in judging the reconstructability of experimentally recorded coherent diffraction patterns.

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Year:  2010        PMID: 21164994      PMCID: PMC3068748          DOI: 10.1364/OE.18.026441

Source DB:  PubMed          Journal:  Opt Express        ISSN: 1094-4087            Impact factor:   3.894


  12 in total

1.  Phase retrieval, error reduction algorithm, and Fienup variants: a view from convex optimization.

Authors:  Heinz H Bauschke; Patrick L Combettes; D Russell Luke
Journal:  J Opt Soc Am A Opt Image Sci Vis       Date:  2002-07       Impact factor: 2.129

2.  Phase retrieval by iterated projections.

Authors:  Veit Elser
Journal:  J Opt Soc Am A Opt Image Sci Vis       Date:  2003-01       Impact factor: 2.129

3.  Methods used in the structure determination of bovine mitochondrial F1 ATPase.

Authors:  J P Abrahams; A G Leslie
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1996-01-01

4.  Phase retrieval algorithms: a comparison.

Authors:  J R Fienup
Journal:  Appl Opt       Date:  1982-08-01       Impact factor: 1.980

5.  Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy.

Authors:  Huaidong Jiang; Changyong Song; Chien-Chun Chen; Rui Xu; Kevin S Raines; Benjamin P Fahimian; Chien-Hung Lu; Ting-Kuo Lee; Akio Nakashima; Jun Urano; Tetsuya Ishikawa; Fuyuhiko Tamanoi; Jianwei Miao
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-04       Impact factor: 11.205

6.  Wavelength choice for soft x-ray laser holography of biological samples.

Authors:  R A London; M D Rosen; J E Trebes
Journal:  Appl Opt       Date:  1989-08-15       Impact factor: 1.980

7.  Quantitative image reconstruction of GaN quantum dots from oversampled diffraction intensities alone.

Authors:  Jianwei Miao; Yoshinori Nishino; Yoshiki Kohmura; Bart Johnson; Changyong Song; Subhash H Risbud; Tetsuya Ishikawa
Journal:  Phys Rev Lett       Date:  2005-08-17       Impact factor: 9.161

8.  Reconstruction of a yeast cell from X-ray diffraction data.

Authors:  Pierre Thibault; Veit Elser; Chris Jacobsen; David Shapiro; David Sayre
Journal:  Acta Crystallogr A       Date:  2006-06-21       Impact factor: 2.290

9.  Effectiveness of iterative algorithms in recovering phase in the presence of noise.

Authors:  Garth Williams; Mark Pfeifer; Ivan Vartanyants; Ian Robinson
Journal:  Acta Crystallogr A       Date:  2006-12-19       Impact factor: 2.290

10.  Data preparation and evaluation techniques for x-ray diffraction microscopy.

Authors:  Jan Steinbrener; Johanna Nelson; Xiaojing Huang; Stefano Marchesini; David Shapiro; Joshua J Turner; Chris Jacobsen
Journal:  Opt Express       Date:  2010-08-30       Impact factor: 3.894

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  4 in total

Review 1.  Methods and application of coherent X-ray diffraction imaging of noncrystalline particles.

Authors:  Masayoshi Nakasako; Amane Kobayashi; Yuki Takayama; Kenta Asakura; Mao Oide; Koji Okajima; Tomotaka Oroguchi; Masaki Yamamoto
Journal:  Biophys Rev       Date:  2020-03-16

2.  Karyotyping human chromosomes by optical and X-ray ptychography methods.

Authors:  Laura Shemilt; Ephanielle Verbanis; Joerg Schwenke; Ana K Estandarte; Gang Xiong; Ross Harder; Neha Parmar; Mohammed Yusuf; Fucai Zhang; Ian K Robinson
Journal:  Biophys J       Date:  2015-02-03       Impact factor: 4.033

3.  Phase retrieval by coherent modulation imaging.

Authors:  Fucai Zhang; Bo Chen; Graeme R Morrison; Joan Vila-Comamala; Manuel Guizar-Sicairos; Ian K Robinson
Journal:  Nat Commun       Date:  2016-11-18       Impact factor: 14.919

4.  Signal enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects.

Authors:  Yuki Takayama; Saori Maki-Yonekura; Tomotaka Oroguchi; Masayoshi Nakasako; Koji Yonekura
Journal:  Sci Rep       Date:  2015-01-28       Impact factor: 4.379

  4 in total

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